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Hypoxia-inducible factor (HIF)-prolyl hydroxylase 3 (PHD3) maintains high HIF2A mRNA levels in clear cell renal cell carcinoma
Most clear cell renal cell carcinomas (ccRCCs) have inactivation of the von Hippel-Lindau tumor suppressor protein (pVHL), resulting in the accumulation of hypoxia-inducible factor -subunits (HIF-) and their downstream ...
Differential ATAC-seq and ChIP-seq peak detection using ROTS
<p> Changes in cellular chromatin states fine-tune transcriptional output and ultimately lead to phenotypic changes. Here we propose a novel application of our reproducibility-optimized test statistics (ROTS) to detect ...
Compressive stress-mediated p38 activation required for ERα + phenotype in breast cancer
<p>Breast cancer is now globally the most frequent cancer and leading cause of women's death. Two thirds of breast cancers express the luminal estrogen receptor-positive (ER alpha + ) phenotype that is initially responsive ...
Benchmarking methods for detecting differential states between conditions from multi-subject single-cell RNA-seq data
<p>Single-cell RNA-sequencing (scRNA-seq) enables researchers to quantify transcriptomes of thousands of cells simultaneously and study transcriptomic changes between cells. scRNA-seq datasets increasingly include multisubject, ...
An Unbiased Functional Genetics Screen Identifies Rare Activating ERBB4 Mutations
<p>Despite the relatively high frequency of somatic <i>ERBB4</i> mutations in various cancer types, only a few activating <i>ERBB4</i> mutations have been characterized, primarily due to lack of mutational hotspots in ...
Estimating cell type-specific differential expression using deconvolution
<p>When differentially expressed genes are detected from samples containing different types of cells, only a very coarse overview without any cell type-specific information is obtained. Although several computational methods ...
scShaper: an ensemble method for fast and accurate linear trajectory inference from single-cell RNA-seq data
<p>Motivation<br>Computational models are needed to infer a representation of the cells, i.e. a trajectory, from single-cell RNA-sequencing data that model cell differentiation during a dynamic process. Although many ...
Computational strategies for single-cell multi-omics integration
<p>Single-cell omics technologies are currently solving biological and medical problems that earlier have remained elusive, such as discovery of new cell types, cellular differentiation trajectories and communication ...